Symbiont communities shape coral physiology and nutrition

CB Wall, M Kaluhiokalani, BN Popp, MJ Donahue, RD Gates. (2019). Divergent symbiont communities determine the physiology and nutrition of a reef coral across a light-availability gradient. The ISME Journal.

Reef corals are mixotrophic organisms relying on symbiont-derived photoautotrophy and water column heterotrophy. Coral endosymbionts (Family: Symbiodiniaceae), while typically considered mutualists, display a range of species-specific and environmentally mediated opportunism in their interactions with coral hosts, potentially requiring corals to rely more on heterotrophy to avoid declines in performance. To test the influence of symbiont communities on coral physiology (tissue biomass, symbiont density, photopigmentation) and nutrition (δ¹³C, δ¹⁵N), we sampled Montipora capitata colonies dominated by a specialist symbiont Cladocopium spp. or a putative opportunist Durusdinium glynnii (hereafter, C- or D-colonies) from Kāne‘ohe Bay, Hawai‘i, across gradients in photosynthetically active radiation (PAR) (1 - 10 m depth) during summer and winter.

Directory information

PanKBay-isotopes_pub.html

html file for Rmd output

PanKBay-isotopes_pub.Rmd

R markdown for project

PanKBay isotopes.Rproj

R project to run Rmd and directory

DATA houses the following folders and files

coast_n83.shp : shape files for making site maps
environmental :

• folder sea level for sea-level correction
  columns
  stationID = Moku o Lo'e weather station
  datum = mean sea level (MSL)
  TimeUTC = time in UTC
  TideHT = tidal height in meters
  (other columns NA)

• folder temp and light for raw data collected on the reef

• PanKBay_nutrients.csv for dissolved inorganic nutrients
  columns
  Date = date of collection
  Reef = reef IDs, F=fringe, R=patch reef
  Location = northwest NW, northeast NE, central west CW, southeast SE, southwest SW
  phosphate, silicate, N+N (nitrate+nitrite), ammonium = all in μmol L-1

• Reefs_lat_long.csv for mapping sampling sites
  columns
  Site = Reef ID as cardinal directions and Reef number
  latitude and longitude = in decimal degrees

qPCR

• eds files (for StepOne Platform) and associated .txt files with qPCR plate reads

• isotopes_SW_all times.csv
  seawater and plankton isotopes collected at the sample sites in each season
  columns
  Season = summer or winter (northern hemisphere)
  Sampling.date = date as "yyyymmdd"
  Reef = F for fringe reef, R for patch reef, and reef number
  Location = NW, SE, NE, SW for north (N) south (S) and east (E) or west (W)
  Region = northern or southern Kāne'ohe Bay
  Habitat.type = fringe or patch reef
  North.South.ID = arbitrary ID #
  SW.fraction..um = the size fraction of seawater in μm
  ug.N = ug of nitrogen
  d15N = δ¹⁵N in permil
  ug.C = ug of carbon
  d13C = δ¹³C in permil

• mastersheet_PanKBAY.csv
  all response variables from physiology and isotope analyses (prior to calculation of C-D dominance)
  columns
  Date = date of collection as mm/dd/yy
  Season = summer or winter (northern hemisphere)
  Reef = F for fringe reef, R for patch reef, and reef number
  Location = NW, SE, NE, SW for north (N) south (S) and east (E) or west (W)
  Reef.type = fringe or patch reef Bay.region = northern or southern Kāne'ohe Bay
  Time.of.collection = time for tidal correction
  Depth..m = colony depth in meters
  Sample.ID = arbitrary sample ID
  total.blastate.ml = total tissue extract (blastate) in ml
  surface.area.cm2 = colony surface area in cm2
  cells.ml = symbiont densities in cells per ml blastate
  ug.chl.a.ml = μg of chlorophyll a per ml blastate
  ug.chl.c2.ml = μg of chlorophyll a per ml blastate
  mg.biomass.ml = mg of host biomass per ml blastate
  host..mass.mg = lyophilized host biomass for isotope analysis
  host..ug.N = μg of nitrogen in host tissue
  host..d15N = δ15N of host tissues in permil
  host..ug.C = μg of carbon in host tissue
  host..d13C = δ13C of host tissues in permil
  host..C.N = molar ratio of carbon : nitrogen in symbiont tissues
  symb..mass.mg = lyophilized symbiont biomass for isotope analysis
  symb..ug.N = μg of nitrogen in symbiont tissue
  symb..d15N = δ15N of symbiont tissues in permil
  symb..ug.C = μg of carbon in host tissue
  symb..d13C = δ13C of symbiont tissues in permil
  symb..C.N = molar ratio of carbon : nitrogen in symbiont tissues
  d15N..host.symb = difference in δ15N of host minus symbiont in permil
  d13C..host.symb = difference in δ13C of host minus symbiont in permil
  d13C..skel = δ13C of coral skeletal carbonates in permil
  d18O.skel = δ18O of coral skeletal carbonates in permil

• PanKBay_summer_qPCR.csv
  compiled qPCR data for summer samples (post pipeline [detailed in Rmd file])

• PanKBay_winter_qPCR
  compiled qPCR data for winter samples (post pipeline [detailed in Rmd file])
  columns
  Colony = arbitrary ID
  Date = mm/dd/yy
  Depth..m = coral depth in meters
  Latitude and Longitude = in decimal degrees
  Time = hh:mm
  Season = summer and winter (northern hemisphere)
  Reef.type = fringe or patch reef
  Bay.region = northern or southern Kāne'ohe Bay
  Reef = reef ID
  Location = NE, NW, SE, SW
  Sample.ID = arbitrary ID for colony at each reef location
  File.Name = the qPCR file where data originated
  C.CT.mean = mean CT value for 2 reps for Cladocopium
  D.CT.mean = mean CT value for 2 reps for Durusdinium
  C.CT.sd = standard deviation CT value for 2 reps for Cladocopium
  D.CT.sd = standard deviation CT value for 2 reps for Durusdinium
  propC = proportion of community as percentage Cladocopium
  propD = proportion of community as percentage Durusdinium
  Dom = dominant symbiont at > 50%
  Mix = mixture of symbionts as all C, all D, D>C or C>D

FIGURES houses exported figures

environmental :

• folder: unused are figures used in analysis but not published

• pdfs for daily light integral (DLI) and photosynthetically active radiation (PAR) at the 2m depth only (for comparison)

• pdf for coefficent plots for DLI and PAR fitting

• all.nutrients.pdf (DIN)

• DLI.bar.pdf (mean +/-SE bar plot)

• DLIcalc.alldepths.pdf (DLI at 3 depth zones)

• iso.sources.KBay.pdf (mean +/- SE, isotope sources, end members)

• KBaymap.pdf (map and sites)

• Temp.allsites.pdf (temperature at 2m for each site)

isotopes :

• isotope_multipanel.pdf (carbon isotope figures)
• suppm.CNboxplot.pdf (boxplots for C:N data, host and symbionts)
• suppm.Cskel.pdf (skeletal carbon and oxygen isotope figures)
• suppm.nitrogen.pdf (nitrogen isotope figures)

models :

• variance.pdf (model random effect [location] proportion of variance)

multivariate :

• PCx4.pdf (PCA with 4 plots of differing categories)

physiology :

• physio_multipanel.pdf (multipanel of all physiology metrics)

regressions :

• symb.isotope_by.symb.phys.pdf (regression of symbiont physiology vs. symbiont carbon isotope values)
• symb.by_HS.d13C.pdf (regression of symbiont physiology vs. carbon host-symbiont isotopes values)

symbionts :

• Light by Depth_symbs.pdf (calculations for DLI at the coral surface)
• Symb_Season_Light_logistic.pdf (logistic regression histograms of symbiont distributions)
• Symbionts_by_Season_depth.pdf (probability of Durusdinium across depth)

M capitata_KBay_Wall.png (coral figure)

OUTPUT houses exported outputs and compiled data

• C_D sample size.csv (sample size for C- and D-dominated corals)
• data.all.csv (all physiology, isotope, and symbiont community data)
• kd.all.csv (light attenuation coefficients for each site)
• Light attenuation_table.csv (light DLI mean +/-SE at <1m and attenuation relative to this at 2m and 8m-depth)
• light coeffs_factor.csv (coefficients of models for ligh-at-depth calculations)
• season.DLI.csv (DLI mean +/- SE at each site, in each season)